* In-: Indicates negation or lack of. Indistinct means unclear or not easily recognized.
* Dis-: Can also indicate negation. Distinguish means to perceive a difference between things.
* Re-: Means "again" or "back". Rediscover means to find something again after it was lost or forgotten.
* Un-: Indicates the opposite of. Undistinct (though not commonly used) could mean "not distinct," or "not clear".
The best prefix will depend on the specific context and the meaning you want to convey.